Does "Run Silent, Run Deep" not warrant even an honorable mention?
Operation Petticoat comes to mind...
Ok, seriously...
The Hunt for Red October is still my favorite, mostly for sentimental reasons.
Das Boot is obvious, though I haven't watched it since video discs were state of the art.
I liked K-19, even if Ford did chew the scenery.
Down Periscope is a guilty pleasure.
Above Us, the Waves and Torpedo Run I'll have to check out.
And don't get me started on U-571 or Crimson Tide.